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Load a Python colormap to FSLeyes

Get RGB colors, one per line, for a given Python colormap. In the script below, we get RGB colors for the jet matplotlib colormap.

import matplotlib.pyplot as plt
import numpy as np

# Generate the jet colormap
cmap = plt.cm.get_cmap('jet')

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Template script for sct_run_batch

This gist contains a template script that can be run across multiple subjects using the sct_run_batch wrapper script.

The template bash script below can be run from you command line using the following command:

sct_run_batch -script example_script.sh -path-data <DATA> -path-output <DATA>_202X-XX-XX -jobs 16

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import os
import glob
import hashlib
import argparse


def compute_checksum(file_path):
    with open(file_path, 'rb') as f:
        file_bytes = f.read()
    return hashlib.md5(file_bytes).hexdigest()

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# Set ITK direction from image1 to image2
#
# Usage:
#	python change_itk_orientation.py <image1> <image2>
# Example:
#	python change_itk_orientation.py sub-001_T1w.nii.gz sub-001_T1w_seg.nii.gz
#
# Jan Valosek
#

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Configuration of ssh connection

Unix and MacOS

Let's say we want to configure an ssh connection between machine alpha and beta.

1. Go to your home folder at machine alpha:

$ cd ~

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Simple workflow of collaboration in small team using git and GitHub

This gist describes example of simple workflow on repository whose changes are tracked by git and GitHub

1) Clone (download repository from GitHub to your computer)

# Go to directory where repository will be cloned (downloaded)
cd ~/Documents
# Clone repository from GitHub

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How to create and use virtual environments (venv and conda)

venv and conda are environment manager tools allowing to create virtual environments. Virtual environment separates the dependencies (Python packages) for different projects. This mean that each project can have its own dependencies. Usage of virtual environments allows you to avoid installing Python packages globally (to the system Python) which could break system tools or other projects.

venv environment

1. Create venv

MacOS or Linux (without or with site-packages)

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Run python script from shell (bash, zsh)

Sometimes, I need to call/run python script with arguments from shell. I use bash or zsh as my shell and following workaround works great for me.

Using shell wrapper

1. Some example python script which I need to run from bash:

my_python_script.py:

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Tips and hacks for plotting in python

This gist containts several useful tips, tricks and hacks for plotting of figures, plots and charts using python (matplotlib and seaborn packages).

Fix warning about matplotlib backend in PyCharm

import matplotlib
matplotlib.use('TkAgg')